Parametric EQ

When I first got my Yamaha RX-V 667 I used the YPAO microphone to set up the speakers parameters.Being disappointed with the end result,mainly because I lost the bass/sub noise I ended up setting the speakers up manually. I have learned a lot since then,mainly by reading and having a bit of a play around.I have come across a page in my manual which allows me to play around with Band/Gain,Freq/Gain and Q/Gain. If I was to use the YPAO mic again would it take care of these settings,I only ask as I am still reading into what these Gains are and do and do not want to really upset what I have things set at now. Thank you.